Header list of 1ago.pdb file
Complete list - 16 202 Bytes
HEADER DNA 25-MAR-97 1AGO
TITLE THE SOLUTION NMR STRUCTURE OF AN (S)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61
TITLE 2 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE THIRD POSITION OF THE CODON 61
TITLE 3 REGION, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*AP*YP*GP*AP*AP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: (S)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 DNA ADDUCT;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3');
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: (S)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 DNA ADDUCT
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DNA DUPLEX, B-DNA, HUMAN N-RAS GENE, CODON 61 SEQUENCE, S-STYRENE
KEYWDS 2 OXIDE ADDUCT, N6-ADENINE ADDUCT, MAJOR GROOVE ADDUCT,
KEYWDS 3 DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
AUTHOR B.FENG,M.P.STONE
REVDAT 3 16-FEB-22 1AGO 1 REMARK SEQRES LINK
REVDAT 2 24-FEB-09 1AGO 1 VERSN
REVDAT 1 20-AUG-97 1AGO 0
JRNL AUTH B.FENG,M.VOEHLER,L.ZHOU,M.PASSARELLI,C.M.HARRIS,T.M.HARRIS,
JRNL AUTH 2 M.P.STONE
JRNL TITL MAJOR GROOVE (S)-ALPHA-(N6-ADENYL)STYRENE OXIDE ADDUCTS IN
JRNL TITL 2 AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61
JRNL TITL 3 SEQUENCE: CONFORMATIONS OF THE S(61,2) AND S(61,3) SEQUENCE
JRNL TITL 4 ISOMERS FROM 1H NMR.
JRNL REF BIOCHEMISTRY V. 35 7316 1996
JRNL REFN ISSN 0006-2960
JRNL PMID 8652508
JRNL DOI 10.1021/BI952526F
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH B.FENG,M.P.STONE
REMARK 1 TITL SOLUTION STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE
REMARK 1 TITL 2 HUMAN N-RAS CODON 61 SEQUENCE REFINED FROM 1H NMR USING
REMARK 1 TITL 3 MOLECULAR DYNAMICS RESTRAINED BY NUCLEAR OVERHAUSER EFFECTS
REMARK 1 REF CHEM.RES.TOXICOL. V. 8 821 1995
REMARK 1 REFN ISSN 0893-228X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 1AGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170793.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 6.9
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; 2QF-COSY; AND TOCSY; :
REMARK 210 NOESY; AND(DO; 05'-D
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : AMX500
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX, X-PLOR, MARDIGRAS, CORMA
REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR
REMARK 210 DYNAMICS/SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : THIS STRUCTURE PROVIDED THE BEST
REMARK 210 -FIT FOR THE NOE DATA BASED ON
REMARK 210 THE RELAXATION MATRIX ANALYSIS
REMARK 210 USING CORMA.
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA A 6 O3' - P - O5' ANGL. DEV. = -36.9 DEGREES
REMARK 500 DA A 6 O3' - P - OP2 ANGL. DEV. = -15.8 DEGREES
REMARK 500 DA A 6 O3' - P - OP1 ANGL. DEV. = 25.5 DEGREES
REMARK 500 DA A 6 OP1 - P - OP2 ANGL. DEV. = -17.3 DEGREES
REMARK 500 DA A 6 O5' - P - OP1 ANGL. DEV. = -33.4 DEGREES
REMARK 500 DA A 6 O5' - P - OP2 ANGL. DEV. = 16.4 DEGREES
REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES
REMARK 500 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DA A 10 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DT B 13 O3' - P - O5' ANGL. DEV. = -38.1 DEGREES
REMARK 500 DT B 13 O3' - P - OP2 ANGL. DEV. = -33.1 DEGREES
REMARK 500 DT B 13 O3' - P - OP1 ANGL. DEV. = 10.9 DEGREES
REMARK 500 DT B 13 OP1 - P - OP2 ANGL. DEV. = -13.7 DEGREES
REMARK 500 DT B 13 O5' - P - OP1 ANGL. DEV. = -15.5 DEGREES
REMARK 500 DT B 13 O5' - P - OP2 ANGL. DEV. = 26.7 DEGREES
REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AGK RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
REMARK 900 RELATED ID: 1AGZ RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
DBREF 1AGO A 1 11 PDB 1AGO 1AGO 1 11
DBREF 1AGO B 12 22 PDB 1AGO 1AGO 12 22
SEQRES 1 A 11 DC DG DG DA DC DA Y DG DA DA DG
SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG
MODRES 1AGO Y A 7 DA
HET Y A 7 49
HETNAM Y 2'-DEOXY-N6-(S)STYRENE OXIDE ADENOSINE MONOPHOSPHATE
FORMUL 1 Y C18 H22 N5 O7 P
LINK O3' DA A 6 P Y A 7 1555 1555 1.63
LINK O3' Y A 7 P DG A 8 1555 1555 1.61
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 16 202 Bytes